Identification and characterization of SSR markers in taro [Colocasia esculenta (L.) Schott] by RAD sequencing

Abstract

Taro [Colocasia esculenta (L.) Schott] is an old crop with high genetic diversity. However, the breeding of taro is limited by the lack of well-developed genetic markers. To help further research on taro germplasm resource management, we developed a set of SSR marker primers. Restriction site-associated DNA sequencing (RAD-seq) was used to identify SSRs from a taro variety. PCR and capillary electrophoresis were applied to evaluate the efficiency of the primers. A phylogenetic tree was constructed to analyse the evolutionary relationship of 30 taro varieties. A total of 4438 SSRs (simple sequence repeats)were identified using RAD sequencing. A total of 3919 pairs of primers were designed based on the SSR data. Trinucleotide repeats (49.1%) were the most abundant type of SSR, while AT was the most common motif type (327 instances). Among 50 randomly selected primer pairs, 46 primer pairs were able to amplify the corresponding bands. A phylogenetic tree cluster analysis using SSR markers mainly supported the classification of taro varieties according to their phenotypes and ecological distribution. The SSR markers identified in this study provide a useful resource for taro genetic and germplasm research and genetic breeding.